ArticleJournal of the American Chemical Society2021
Predicting Mutational Effects on Receptor Binding of the Spike Protein of SARS-CoV-2 Variants.
Article in Journal of the American Chemical Society, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- Predicting the trend of SARS-CoV-2 mutation frequencies using historical data.Bioinformatics (Oxford, England) · 2025Article
- Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights.Biophysical reviews · 2025Review
- Key Interaction Changes Determine the Activation Process of Human Parathyroid Hormone Type 1 Receptor.Journal of the American Chemical Society · 2025Article
- Exploring SARS-CoV-2 spike protein mutations through genetic algorithm-driven structural modeling.Bioinformatics advances · 2025Article
- Exploring the Activation Process of the Glycine Receptor.Journal of the American Chemical Society · 2024Article
- Article
- Exploring the activation mechanism of metabotropic glutamate receptor 2.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2.ACS nanoscience Au · 2024Article
- Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks.Nature communications · 2024Article
- Nanobody engineering for SARS-CoV-2 neutralization and detection.Microbiology spectrum · 2024Article
- PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information.Briefings in bioinformatics · 2024Article
- The Diverse Nature of the Molecular Interactions That Govern the COV-2 Variants' Cell Receptor Affinity Ranking and Its Experimental Variability.International journal of molecular sciences · 2024Article
- Advances in nanobiosensors during the COVID-19 pandemic and future perspectives for the post-COVID era.Nano convergence · 2024Review
- Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective.ACS omega · 2023Review
- Early warning of emerging infectious diseases based on multimodal data.Biosafety and health · 2023Review
- Programmable DNA biocomputing circuits for rapid and intelligent screening of SARS-CoV-2 variants.Biosensors & bioelectronics · 2023Article
- Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics.International journal of molecular sciences · 2023Review
- Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants.PLoS computational biology · 2023Article
- TEMPO: A transformer-based mutation prediction framework for SARS-CoV-2 evolution.Computers in biology and medicine · 2023Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
The pandemic caused by SARS-CoV-2 has cost millions of lives and tremendous social/financial loss. The virus continues to evolve and mutate. In particular, the recently emerged "UK", "South Africa", and Delta variants show higher infectivity and spreading speed. Thus, the relationship between the mutations of certain amino acids and the spreading speed of the virus is a problem of great importance. In this respect, understanding the mutational mechanism is crucial for surveillance and prediction of future mutations as well as antibody/vaccine development. In this work, we used a coarse-grained model (that was used previously in predicting the importance of mutations of N501) to calculate the free energy change of various types of single-site or combined-site mutations. This was done for the UK, South Africa, and Delta mutants. We investigated the underlying mechanisms of the binding affinity changes for mutations at different spike protein domains of SARS-CoV-2 and provided the energy basis for the resistance of the E484 mutant to the antibody m396. Other potential mutation sites were also predicted. Furthermore, the in silico predictions were assessed by functional experiments. The results establish that the faster spreading of recently observed mutants is strongly correlated with the binding-affinity enhancement between virus and human receptor as well as with the reduction of the binding to the m396 antibody. Significantly, the current approach offers a way to predict new variants and to assess the effectiveness of different antibodies toward such variants.
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Registered trials
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